Fig. 5: Landscape of the bone marrow microenvironment in TC-RK mice.

a Uniform manifold approximation and projection (UMAP) visualizations of unsupervised clustering analysis of all cells that passed quality filtering. Cells are colored according to their genotype in the upper row and according to their Sdc1, Cd19, Tnfrsf17 and Slamf7 expression respectively below. b UMAP visualization of annotated clusters (left) and frequency of clusters (right) in RK (pooled from 3 mice) and TC-RK (pooled from 4 mice) derived BM cells. Plasma cells are highlighted with a green circle in the UMAP. c Differential abundance (DA) analysis for changes in cluster abundance (left) and log-fold change for each annotated cluster (right). Plasma cell cluster is highlighted by a green circle (left) or a green arrow (right). d Gene expression dot plot depicts the percent and average expression of B-cell markers within the B and plasma cell subcluster. e UMAP visualization of unsupervised clustering analysis of B-cells and plasma cells (defined by Sdc1 and Slamf7 expression). Cells are color coded according to their genotype (left) or according to Sdc1, Jchain, Prdm1 and Xpb1 expression respectively (right). f Gene expression profile visualize the percent and average expression of T-cell markers within the T-cell cluster. g Gene set enrichment analysis (GSEA) plot for CD8 T-cell exhaustion enriched T-cells from TC-RK mice (top) and GSEA plot of naive CD8 T-cells enriched in T-cells of RK mice (bottom).